2024-05-22 REL PDBe PDBe PDBe 2019-08-12 2020-04-08 2020-04-08 2024-05-22 French National Research Agency ANR-15-CE11-0021-01 France French National Research Agency ANR-16-CE11-0007-01 France French National Research Agency Labex: ANR-10-LABX- 0036_NETRNA France Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus Khusainov I Pellegrino S Yusupova G Yusupov M Fatkhullin B Stress, S.aureus, RsfS, Hibernation, RIBOSOME Khusainov I Fatkhullin B Pellegrino S Bikmullin A Liu WT Gabdulkhakov A Shebel AA Golubev A Zeyer D Trachtmann N Sprenger GA Validov S Usachev K Yusupova G Yusupov M Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach. Nat Commun UK 11 1656 1656 2020 32245971 doi:10.1038/s41467-020-15517-0 2041-1723 6sj6 FULLOVERLAP 50S ribosomal subunit complex with stress induced ribosome silencing factor RsfS from Staphylococcus aureus 50S ribosomal subunit complex with stress induced ribosome silencing factor RsfS from Staphylococcus aureus 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 1.35 50S ribosomal subunit 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Staphylococcus aureus subsp. aureus NCTC 8325 Ribosomal silencing factor RsfS 1 26 Staphylococcus aureus subsp. aureus NCTC 8325 23S ribosomal RNA Staphylococcus aureus (strain NCTC 8325) 0.946696625 1 GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUG GGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUG AAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCC CUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGU UACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUC UCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACU CUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAA CCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUG AUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGA AACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUG AGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUA GCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCC GAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCA GCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCC AUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAA GCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCU UAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAG GCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUA CCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUA AGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGUGUCUUCGAGUCGUUGA UUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAU UCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUUUAGG GUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGU GAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCC CCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGG CGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGG ACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUG AAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAU CGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUC CCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGU CGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACA GGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGU CGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCU AUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCA GUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCU CAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGA CAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA CP039156.1 5S ribosomal RNA Staphylococcus aureus (strain NCTC 8325) 0.036974944999999995 1 UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCCUUAGCGUCGAUGGUAGUCG AACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGC CP035671.1 50S ribosomal protein L2 Staphylococcus aureus (strain NCTC 8325) 0.030217163999999998 1 LEVO MAIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGINAKVDS IQYDPNRSANIALVVYADGEKRYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGGQIARSAGA SAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHELVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP IGRPSPMSPWGKPTLGKKTRRGKKSSDKLIVRGRKKK P60430 50S ribosomal protein L3 Staphylococcus aureus (strain NCTC 8325) 0.023760256 1 LEVO MTKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQVGFEDKKAYKKDAKSNKYANKPAEGHAKKA DAAPKRFIREFRNVDVDAYEVGQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAPGSVGMASDA SRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNVPGPKKGLVEIRTSIKKGNK Q2FW06 50S ribosomal protein L4 Staphylococcus aureus (strain NCTC 8325) 0.022495697 1 LEVO MANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRA PQWRGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVVTENED VNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKKVEEVLG Q2FW07 50S ribosomal protein L13 Staphylococcus aureus (strain NCTC 8325) 0.016359427 1 LEVO MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSN HPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG Q2FW38 50S ribosomal protein L14 Staphylococcus aureus (strain NCTC 8325) 0.013157342 1 LEVO MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFD ENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL Q2FW16 50S ribosomal protein L15 Staphylococcus aureus (strain NCTC 8325) 0.01562889 1 LEVO MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLD QLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI P0A0F8 50S ribosomal protein L16 Staphylococcus aureus (strain NCTC 8325) 0.016274049 1 LEVO MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLE VRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREELGGETNES Q2FW13 50S ribosomal protein L17 Staphylococcus aureus (strain NCTC 8325) 0.013771773 1 LEVO MGYRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQT ALQKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV Q2FW33 50S ribosomal protein L18 Staphylococcus aureus (strain NCTC 8325) 0.013124093 1 LEVO MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAI AKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF Q2FW22 50S ribosomal protein L19 Staphylococcus aureus (strain NCTC 8325) 0.013392771 1 LEVO MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHT PKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR Q2FZ42 50S ribosomal protein L20 Staphylococcus aureus (strain NCTC 8325) 0.013720294999999999 1 LEVO MPRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLM NGLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDALK Q2FXQ1 50S ribosomal protein L21 Staphylococcus aureus (strain NCTC 8325) 0.011354081 1 LEVO MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYKRRK NSKRKKGHRQPYTKLTIDKINA Q2FXS8 50S ribosomal protein L22 Staphylococcus aureus (strain NCTC 8325) 0.012857921999999999 1 LEVO MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGP TLKRFRPRAQGRASAINKRTSHITIVVSDGKEEAKEA Q2FW11 50S ribosomal protein L23 Staphylococcus aureus (strain NCTC 8325) 0.010625398 1 LEVO MEARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIV TLKEGSIDLFN Q2FW08 50S ribosomal protein L24 Staphylococcus aureus (strain NCTC 8325) 0.011561504 1 LEVO MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPEGGILETEAAIHVSNVQLLDPKTNEPTR VGYKFVDGKKVRIAKKSGEEIKSNN Q2FW17 50S ribosomal protein L25 Staphylococcus aureus (strain NCTC 8325) 0.023810609 1 LEVO MASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFD PLKNQITHIDFLAINMSEERTVEVPVQLVGEAVGAKEGGVVEQPLFNLEVTATPDNIPEAIEVDITELNINDSLTVADVK VTGDFKIENDSAESVVTVVAPTEEPTEEEIEAMEGEQQTEEPEVVGESKEDEEKTEE Q2G0S0 50S ribosomal protein L27 Staphylococcus aureus (strain NCTC 8325) 0.010334798000000001 1 LEVO MLKLNLQFFASKKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERK GRDKKQVSVYAVAE Q2FXT0 50S ribosomal protein L28 Staphylococcus aureus (strain NCTC 8325) 0.006995288999999999 1 LEVO MGKQCFVTGRKASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVTRV Q2FZ60 50S ribosomal protein L29 Staphylococcus aureus (strain NCTC 8325) 0.008105266 1 LEVO MKAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKANQ Q2FW14 50S ribosomal protein L30 Staphylococcus aureus (strain NCTC 8325) 0.006565683 1 LEVO MAKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK P0A0G2 50S ribosomal protein L32 Staphylococcus aureus (strain NCTC 8325) 0.0066578029999999995 1 LEVO MAVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGREYKLSHRVCKNCGSYNGEEVAAK Q2FZF1 50S ribosomal protein L34 Staphylococcus aureus (strain NCTC 8325) 0.005454642 1 LEVO MVKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLSA Q2FUQ0 50S ribosomal protein L35 Staphylococcus aureus (strain NCTC 8325) 0.007722368 1 LEVO MPKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYKK Q2FXQ0 Ribosomal silencing factor RsfS Staphylococcus aureus (strain NCTC 8325) NCTC 8325 0.013497068 1 Escherichia coli BL21(DE3) LEVO MNSQELLAIAVDAIDNKKGEDTISLEMKGISDMTDYFVVTHGNNERQVQAIARAVKEVANEQNIEVKRMEGYNEARWILI DLADVVVHVFHKDERNYYNIEKLYQDAPLESYSQVAY Q2G298 MAGNESIUM ION 2.4305e-05 56 MG POTASSIUM ION 3.9098e-05 3 K singleParticle particle 0.7 7.5 10.0 C8H18N2O4S Hepes 50.0 KCl potassium chloride 10.0 NH4Cl ammonium chloride 10.0 Mg(CH3OO)2 magnesium acetate Quantifoil R2/2 COPPER 400 GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 3.0 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) 2 1856 43.0 24.6 1 172729 EMD-6177 C1 3.23 FSC 0.143 CUT-OFF RELION 2.1 83885 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 RELION 2.1 emd_10212.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 300.3 300.3 300.3 90.0 90.0 90.0 X Y Z -0.10070784 0.16990301 0.0009123183 0.006633047 0.858 0.858 0.858 0.027 AUTHOR Cryo-EM map of 50S-RsfS complex from Staphylococcus aureus 5LI0 PDB experimental model FLEXIBLE FIT REAL